The Role of Genetic Testing in Tolvaptan Decision Making: A Case of Atypical Cystic Kidney Disease Associated With CYP24A1

Abstract

Autosomal dominant polycystic kidney disease (PKD) is a genetically heterogenous group of disorders, most often caused by mutations in polycystin-1 (PKD1) or polycystin-2 (PKD2), for which tolvaptan is the only Food and Drug Administration--approved therapy to slow disease progression in rapidly progressive cases. However, atypical genetic causes of cystic kidney disease present unique diagnostic and therapeutic challenges, as these patients may have recessive forms of PKD that are poorly represented in clinical trials and not approved for tolvaptan. We present the case of a 45-year-old man with bilateral kidney cysts initially diagnosed with autosomal dominant PKD and referred for a second opinion regarding tolvaptan initiation. Comprehensive genetic testing revealed homozygous CYP24A1 missense mutations (c.1147G>C, p.Glu383Gln). Although traditionally associated with infantile hypercalcermia, CYP24A1 deficiency has been recently described in a case series of patients with cystic kidney disease. Laboratory findings confirmed elevated 1,25-dihydroxyvitamin D levels associated with suppressed parathyroid hormone and hypercalciuria. Given the absence of evidence supporting tolvaptan efficacy in this patient's recessive form of PKD, combined with the side effects and cost of the drug, therapy was not recommended. This case underscores the critical role of genetic testing in differentiating etiologies of cystic kidney disease, for personalized management strategies that minimize risk and expense.

Introduction

Cystic kidney disease has many etiologies with often overlapping clinical features, including bilateral kidney cysts, renal enlargement, and progressive kidney dysfunction. Autosomal dominant polycystic kidney disease (ADPKD) is the most common hereditary form of cystic kidney disease and is typically caused by germline mutations in PKD1 or PKD2 genes.¹ For patients with rapidly progressive ADPKD, the vasopressin V2 receptor antagonist tolvaptan is the only Food and Drug Administration--approved therapy.² However, its efficacy is not well established for atypical forms of the disease arising from recessive cystic kidney disease. When clinical presentations are ambiguous, genetic testing can be an invaluable tool for refining diagnosis and guiding treatment. In this study, we describe a unique case of cystic kidney disease associated with CYP24A1 mutations, in which genetic findings were pivotal in the decision-making process regarding tolvaptan therapy.

Case Report

A 45-year-old man presented for a second opinion regarding tolvaptan therapy. He previously was found to have diffuse kidney cysts in the medullary and corticomedullary junction, incidentally identified on magnetic resonance imaging (Fig 1). His baseline serum creatinine has been 1.0 mg/dL with a correlate estimated glomerular filtration rate of >90 mL/min/1.73 m², without discernible decline over the preceding 3 years. Urinalysis lacked dipstick hematuria and proteinuria, whereas his quantified urinary albumin-creatinine ratio was below the sensitivity of detection. His family history included a full biological brother diagnosed with PKD without known chronic kidney disease. His biological father died of a cerebrovascular hemorrhage in his seventh decade of life, without known kidney cysts or chronic kidney disease. His biological mother had recurrent urinary tract infections owing to a reported congenital anomaly of the kidney and urinary tract. The patient had previously been diagnosed with ADPKD and was prescribed tolvaptan locally. He expressed concerns about the potential side effects, including polyuria, polydipsia, and hepatotoxicity.

Figure 1.

Bilateral kidney cysts on MRI. Coronal T2-weighted MRI demonstrating multiple bilateral kidney cysts in the medullary and corticomedullary junction is shown. Abbreviation: MRI, magnetic resonance imaging.

Genetic testing involved whole-genome short-read sequencing using Illumina-based tagmentation (Mayo Clinic laboratories) followed by next-generation sequencing targeting a custom panel of 437 genes associated with monogenic kidney disease, including well-described kidney cystic disorder genes PKD1, PKD2, GANAB, DNAJB11, IFT140, NEK8, ALG5, ALG6, ALG8, ALG9, PKHD1, and DZIP1L (Variantyx Mayo Kidney Disease--Custom Analysis, Mayo Clinic laboratories). The employed genome-based approach adds characterization of intronic variants in addition to traditional sequence analysis for single-nucleotide variants, deletions, and insertions. In addition, a proprietary capture-based next-generation sequencing panel (Variantyx Mayo Kidney Disease--Custom Analysis, Mayo Clinic laboratories) was used to detect genomic differences that differentiate PKD1 pseudogene homology (exons 1-33) from its 6 pseudogenes (PKD1P1-PKD1P6). Ambiguous results in this short-read approach may prompt confirmatory orthogonal long-read sequencing as needed (PromethION 24; Oxford Nanopore Technologies).

Genetic testing identified biallelic CYP24A1 mutations, homozygous for c.1147G>C(p.Glu383Gln), a rare variant with a maximum allele frequency of 0.03% in nonfounder control populations according to gnomAD, yielding an estimated occurrence of biallelic inheritance of less than 1 in 111 million individuals. The patient’s missense variant, c.1147G>C(p.Glu383Gln), has been identified as part of compound heterozygous states in at least 2 unrelated individuals with autosomal recessive infantile hypercalcemia 1.^3,4 It is located within a critical functional domain of the CYP24A1 protein, a known hotspot for pathogenic mutations.^4,5 These findings, along with the low frequency in databases, classified the variant as likely pathogenic for autosomal recessive infantile hypercalcemia type 1. The patient’s homozygosity for a rare variant was suggestive of consanguinity, often instrumental in identifying conditions of autosomal recessive inheritance.

CYP24A1 encodes the 24-hydroxylase enzyme that degrades the biologically active form of vitamin D, 1,25-dihydroxyvitamin D, and its storage form, 25-hydroxyvitamin D, converting them to inactive metabolites for excretion. By doing so, CYP24A1 helps maintain calcium and phosphorus homeostasis, preventing hypercalcemia, and supporting bone health. In infantile hypercalcemia type 1, biallelic pathogenic variants lead to a loss of enzymatic function, resulting in reduced inactivation. Subsequent accumulation of active vitamin D metabolites enhances intestinal calcium absorption to cause hypercalcemia and hypercalciuria associated with nephrolithiasis and nephrocalcinosis, and suppresses parathyroid hormone secretion.⁶ The CYP24A1 enzyme is expressed in multiple tissues but is found in the highest levels in the kidney, where it contributes to both renal and systemic regulation of circulating vitamin D hormones.

A more recent case series has implicated CYP24A1 deficiency with inheritable cystic kidney disease.⁷ Suspected cases were identifed by correlating genetic variants in CYP24A1 using clinical genetic testing from Mayo Clinic medical records or using research genetic testing provided by the Rare Kidney Stone Consortium CP24A1 Deficiency Registry, with characteristic clinical parameters including elevated 1,25-dihydroxyvitamin D, hypercalciuria, hypercalcemia, nephrolithiasis, and nephrocalcinosis. Medullary and/or corticomedullary junction cysts were present in all 16 patients with confirmed pathogenic variants, as well as 4 of 5 patients with suspected but unconfirmed pathogenic variants. The authors concluded an overall 100% prevalence in their cohort of genetically confirmed cases. The majority of patients with CYP24A1-related cystic kidney disease had biallelic loss-of-function variants similar to that in our patient, whose cystic distribution mirrored those of patients in the case series. In our patient, laboratory tests showed high-normal serum calcium and elevated 1,25-dihydroxyvitamin D (10.1 mg/dL and 80.4 pg/mL, respectively), with normal 25-hydroxyvitamin D and suppressed parathyroid hormone (58.6 ng/mL and 10.3 pg/mL, respectively). A 24-hour urine collection confirmed hypercalciuria with urinary calcium excretion of 592 mg, more than 2-fold above the reference range (<250 mg), associated with calcium oxalate supersaturation. Collective blood and urine laboratories remain consistent with calcitriol-mediated hypervitaminosis D owing to impaired CYP24A1-mediated catabolism.

Given the limited evidence supporting the efficacy of tolvaptan in atypical mutations,^8,9 the side effects, and cost, the patient was advised against initiating therapy. A multidisciplinary discussion emphasized the need for regular monitoring and alternative supportive care strategies. The patient was educated on his genetic findings and their implications for disease progression. He was advised to continue regular nephrology follow-ups, focusing on blood pressure control, dietary management, avoidance of vitamin D supplementation, enhanced fluid intake for kidney stone prevention, and screening for nephrocalcinosis.

Discussion

Loss-of-function variants in CYP24A1 are classically associated with hypercalcemia and hypercalciuria due to abherrent vitamin D metabolism, the related complications of which may present at differing ages. The infantile form is characterized by severe hypercalcemia, failure to thrive, vomiting, dehydration, hypercalciuria, nephrocalcinosis, and nephrolithiasis, which can lead to kidney damage and developmental delays if untreated. When identified in adults, disease is milder and has been associated with an overall 100% prevalence of medullary and/or corticomedullary cystic kidney disease in a recent case series.⁷ Although this specific CYP24A1 mutation, c.1147G>C(p.Glu383Gln), has been associated with the more severe infantile form in compound heterozygous states, our patient’s homozygosity associated with a mild adult-onset form favors this being a hypomorphic mutation.

The mechanism by which CYP24A1 mutations contribute to cyst formation remains unclear but may involve disruptions in calcium metabolism, tubular injury, or nephron remodeling. Future studies could investigate these pathways to clarify the pathophysiology and expand our understanding of atypical pathogenic variants associated with an ADPKD-like phenotype. A recent study proposed that renal tubular calcium oxalate crystal deposition can induce rapid tubular dilation, stimulate signaling pathways linked to PKD, and thereby accelerate cyst formation and disease progression. The researchers concluded that hypercalciuria and crystal deposition might play a role in the development of kidney cysts.¹⁰ As established in the case report, the patient’s impaired vitamin D metabolism and resulting hypercalciuria may contribute to cyst formation through this mechanism, a hypothesis that calls for further investigation in patients with CYP24A1 deficiency.

The Mayo Clinic Image Classification was developed to predict renal prognosis in ADPKD. It is based on a consistent exponential increase in height-adjusted total kidney volume.¹¹ By categorizing patients based on typical or atypical imaging patterns and stratifying progression rates, the Mayo Clinic Image Classification serves as a valuable tool in clinical practice and research. However, some atypical mutations show discordance between cystic burden and kidney function. This lack of alignment raises questions about the adequacy of existing prognostic tools for atypical cases. The limitations of current imaging techniques for these mutations underscore the need for alternative stratification methods or novel biomarkers that better correlate with disease progression. In cases in which imaging findings do not align with the clinical trajectory, genetic testing becomes essential for identifying atypical mutations and refining prognostic and management strategies.

The decision to recommend against tolvaptan therapy was multifactorial. Tolvaptan, a selective vasopressin V2-receptor antagonist, slows cyst growth in typical ADPKD by inhibiting the cAMP pathway, which drives cystic epithelial cell proliferation and chloride-dependent fluid secretion.² However, this benefit has not been demonstrated in recessive cystic kidney disease. Furthermore, the drug is associated with significant adverse effects, including polyuria, polydipsia, and xerostomia owing to its aquaretic action, as well as a risk of hepatotoxicity requiring regular monitoring of liver function tests. Improper use may also lead to hypernatremia.¹² Given the lack of efficacy data for this patient’s specific genetic condition, the potential risks and financial costs outweighed the speculative benefits.

Despite their rarity, non-PKD1/PKD2 mutations should be recognized as potential underlying causes in cystic kidney disease patients, even when the imaging presentation appears typical. This case serves as a powerful example of the value of integrating genetic testing into clinical practice. By identifying the underlying CYP24A1 mutations, clinicians were able to move beyond a standard treatment algorithm and tailor a management plan that was safer and more appropriate for the patient’s specific condition. It highlights the need for clinicians to consider atypical genetic causes in patients with cystic kidney disease and to adapt management strategies through a patient-centered approach.